baldrik,
I believe you are encountering this problem because once the LabVIEW application runs and loads the VI with the MATLAB® script node the connection is made to the MATLAB software and everything is loaded into memory. If you change your file, it will not do anything because the original file is still in memory.
One suggestion would be to have your MATLAB script node in a sub-vi that you can call by reference, and terminate and re-call via your UI. This way a new connection will be made to the MATLAB software and re-load the newly edited .m file.
See this KB for reference. I know the KB references an error, but this is something that can happen if you use this method.
Let me know if you have any additional questions.
MATLAB is a registered trademark of The MathWorks, Inc.
Regards,
Jared Boothe
Staff Hardware Engineer
National Instruments